A new cam, lifters, front cover, valley cover, cam gear and other odds and ends. The cam lobes are differen't on the DoD/AFM cylinders.
To me going to a GEN 4 motor would be my last resort, yes they make more power in stock form and have a way better intake manifold than a 99-07 truck but I dislike the extra parts needed to make power and the more complicated computers they use.
A garden variety LM7 gen 3 motor with a either a cable pcm or a DBW pcm are 5x easier to tune and deal with.